"The decision to recognise Kosovo .... is the result of thorough political assessment," the joint statement issued in Skopje following a government session said.
Antonio Milososki, Macedonia's foreign minister, said his government hoped "it will be understood by Belgrade".
Milan Rocen, Montenegro's foreign minister, echoed that view, saying: "We hope that our relations with Serbia will remain friendly."
But Serbia immediately said it would ask Montenegro's ambassador to leave the country.
Vuk Jeremic, Serbia's foreign minister, said his government considered it "to be an adequate response".
Aleksandr Konuzin, Russia's ambassador to Serbia, said Montenegro and Macedonia were "being blackmailed by certain states which threaten to make problems for their European integration".
For months the Macedonian government has been under pressure from its ethnic Albanian minority, which makes up a third of its two million population, to recognise Kosovo, which is largely ethnically Albanian.
Serbia lost control over Kosovo in 1999 after Nato bombed the country to stop the killing of civilians in a two-year war.
Serbia recalled ambassadors from all 48 countries that recognised Kosovo's February 17 declaration of independence, but decided on Thursday to reinstate ambassadors to all those countries, including the US.